The United States has accused Pakistan’s main spy agency of deliberately undermining Nato efforts in Afghanistan by helping the Taliban and Al-Qaeda militants they are supposed to be fighting.

President George W Bush confronted Yusuf Raza Gillani, Pakistan’s prime minister, in Washington last week with evidence of involvement by the ISI, its military intelligence, in a deadly attack on the Afghan capital and warned of retaliation if it continues.

The move comes amid growing fears that Pakistan’s tribal areas are turning into a global launch pad for terrorists.

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Gillani, on his first official US visit since being elected in February, was left in no doubt that the Bush administration had lost patience with the ISI’s alleged double game.

Bush warned that if one more attack in Afghanistan or elsewhere were traced back to Pakistan, he would have to take “serious action”.

Gillani also met Michael Hayden, director of the CIA, who confronted him with a dossier on ISI support for the Taliban. The key evidence concerned last month’s bombing of the Indian embassy in Kabul, which killed 54 people, including the military attaché.

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An intercepted telephone conversation apparently revealed that ISI agents masterminded the operation. The United States also claimed to have arrested an ISI officer inside Afghanistan.

Yesterday ministers said they had left Washington reeling from what they described as a “grilling” and shocked at “the trust deficit” between Pakistan and its most important backer.

“They were very hot on the ISI,” said a member of the Pakistan delegation. “Very hot. When we asked them for more information, Bush laughed and said, ‘When we share information with your guys, the bad guys always run away’.”